Hello.
Probably that will not be related with the original problem but that's
something that came to me when reviewing the tpi.c code:
In line 583 (and follow), it is stated:
if (epot != epot || epot*beta < bU_neg_limit)
{
if (debug)
{
fprintf(debug,"\n time %.3f, step %d:
non-finite energy %f, using exp(-bU)=0\n",t,step,epot);
}
embU = 0;
}
And maybe the condition (after ||) should be:
if (epot != epot || -epot*beta < bU_neg_limit)
Otherwise we could be making a huge number (>exp(50)) equal to 0 instead
of making exp(-50)=0 as intended, isn't it?
Well, I know I could be a bit confused
Javier
El 09/09/10 17:19, Berk Hess escribió:
Hi,
I realized now that this is an SSE issue.
Normally you would get NAN (or is it INF?). That is treated correctly
in the GROMACS TPI code.
But in SSE a float "wraps around" when it overflows, which could, in
very few cases, lead to a reasonably
looking energy value (I check for very high and very low values).
I found that you can check for overflows in SSE and committed a fix
for 4.5.2.
I also filled the first 10 points (up to r=0.02 nm) of the
potential/force tables, these used to be zero.
These values are only relevant for energy minimization or TPI with
extreme atomic overlap.
Berk
------------------------------------------------------------------------
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Overflow problem with test-particle insertion
Date: Thu, 9 Sep 2010 09:39:42 +0200
Hi,
This is an interesting issue.
The chance is quite small that this happens, but maybe not negligible.
In single precision the maximum a float can store is 2^127.
This gives a minimum distance of (2^127)^-1/12 = 6.5e-4 nm.
The chance of inserting a particle within this radius is dens*3e-10,
where dens is the number of particles per nm^3.
A typical density of LJ particles is 30 per nm^3, which leads to a
chance of 1e-8.
Such insertion numbers can be reached, so we probably have to worry
about this.
However, in your example the distance seems to be around 4e-3, which would
give r^-12 = 6e28. This still fits in a float and should not cause
problems.
So we should make sure we understand what's going on here.
Could you file a bugzilla with the files to reproduce this and which
insertion
is the problematic one?
I so two possible solutions:
Force tabulated potentials with TPI, this can currently be achieved by
setting
the environment variable GMX_FORCE_TABLES
Or require double precision.
But I think both solutions would lead to about 40% lower performance.
Berk
------------------------------------------------------------------------
Date: Wed, 8 Sep 2010 21:16:46 -0400
From: kd...@princeton.edu
To: gmx-users@gromacs.org
Subject: [gmx-users] Overflow problem with test-particle insertion
Hello Gromacs users,
I sent a message to the list in June describing what appeared to be a
float overflow issue with the energy calculation for test-particle
insertions:
http://lists.gromacs.org/pipermail/gmx-users/2010-June/052213.html.
I have recently tried the test-particle insertion mode in
Gromacs-4.5.1, and it seems the problem is still there. Does anyone
know how to work around or fix this problem without using tabulated
potentials?
-Kevin
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--
Javier CEREZO BASTIDA
Estudiante de Doctorado
---------------------
Dpto. Química-Física
Universidad de Murcia
30100 MURCIA (España)
Tlf.(+34)868887434
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